A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses.
Identifieur interne : 000465 ( PubMed/Corpus ); précédent : 000464; suivant : 000466A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses.
Auteurs : Tavis K. Anderson ; Catherine A. Macken ; Nicola S. Lewis ; Richard H. Scheuermann ; Kristien Van Reeth ; Ian H. Brown ; Sabrina L. Swenson ; Gaëlle Simon ; Takehiko Saito ; Yohannes Berhane ; Janice Ciacci-Zanella ; Ariel Pereda ; C Todd Davis ; Ruben O. Donis ; Richard J. Webby ; Amy L. VincentSource :
- mSphere [ 2379-5042 ]
Abstract
The H1 subtype of influenza A viruses (IAVs) has been circulating in swine since the 1918 human influenza pandemic. Over time, and aided by further introductions from nonswine hosts, swine H1 viruses have diversified into three genetic lineages. Due to limited global data, these H1 lineages were named based on colloquial context, leading to a proliferation of inconsistent regional naming conventions. In this study, we propose rigorous phylogenetic criteria to establish a globally consistent nomenclature of swine H1 virus hemagglutinin (HA) evolution. These criteria applied to a data set of 7,070 H1 HA sequences led to 28 distinct clades as the basis for the nomenclature. We developed and implemented a web-accessible annotation tool that can assign these biologically informative categories to new sequence data. The annotation tool assigned the combined data set of 7,070 H1 sequences to the correct clade more than 99% of the time. Our analyses indicated that 87% of the swine H1 viruses from 2010 to the present had HAs that belonged to 7 contemporary cocirculating clades. Our nomenclature and web-accessible classification tool provide an accurate method for researchers, diagnosticians, and health officials to assign clade designations to HA sequences. The tool can be updated readily to track evolving nomenclature as new clades emerge, ensuring continued relevance. A common global nomenclature facilitates comparisons of IAVs infecting humans and pigs, within and between regions, and can provide insight into the diversity of swine H1 influenza virus and its impact on vaccine strain selection, diagnostic reagents, and test performance, thereby simplifying communication of such data. IMPORTANCE A fundamental goal in the biological sciences is the definition of groups of organisms based on evolutionary history and the naming of those groups. For influenza A viruses (IAVs) in swine, understanding the hemagglutinin (HA) genetic lineage of a circulating strain aids in vaccine antigen selection and allows for inferences about vaccine efficacy. Previous reporting of H1 virus HA in swine relied on colloquial names, frequently with incriminating and stigmatizing geographic toponyms, making comparisons between studies challenging. To overcome this, we developed an adaptable nomenclature using measurable criteria for historical and contemporary evolutionary patterns of H1 global swine IAVs. We also developed a web-accessible tool that classifies viruses according to this nomenclature. This classification system will aid agricultural production and pandemic preparedness through the identification of important changes in swine IAVs and provides terminology enabling discussion of swine IAVs in a common context among animal and human health initiatives.
DOI: 10.1128/mSphere.00275-16
PubMed: 27981236
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses.</title><author><name sortKey="Anderson, Tavis K" sort="Anderson, Tavis K" uniqKey="Anderson T" first="Tavis K" last="Anderson">Tavis K. Anderson</name><affiliation><nlm:affiliation>Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Macken, Catherine A" sort="Macken, Catherine A" uniqKey="Macken C" first="Catherine A" last="Macken">Catherine A. Macken</name><affiliation><nlm:affiliation>Bioinformatics Institute, University of Auckland, Auckland, New Zealand.</nlm:affiliation></affiliation></author><author><name sortKey="Lewis, Nicola S" sort="Lewis, Nicola S" uniqKey="Lewis N" first="Nicola S" last="Lewis">Nicola S. Lewis</name><affiliation><nlm:affiliation>Department of Zoology, University of Cambridge, Cambridge, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Scheuermann, Richard H" sort="Scheuermann, Richard H" uniqKey="Scheuermann R" first="Richard H" last="Scheuermann">Richard H. Scheuermann</name><affiliation><nlm:affiliation>J. Craig Venter Institute, La Jolla, California, USA; Department of Pathology, University of California, San Diego, California, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Van Reeth, Kristien" sort="Van Reeth, Kristien" uniqKey="Van Reeth K" first="Kristien" last="Van Reeth">Kristien Van Reeth</name><affiliation><nlm:affiliation>Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.</nlm:affiliation></affiliation></author><author><name sortKey="Brown, Ian H" sort="Brown, Ian H" uniqKey="Brown I" first="Ian H" last="Brown">Ian H. Brown</name><affiliation><nlm:affiliation>Animal and Plant Health Agency, Weybridge, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Swenson, Sabrina L" sort="Swenson, Sabrina L" uniqKey="Swenson S" first="Sabrina L" last="Swenson">Sabrina L. Swenson</name><affiliation><nlm:affiliation>National Veterinary Services Laboratories, USDA-APHIS, Ames, Iowa, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Simon, Gaelle" sort="Simon, Gaelle" uniqKey="Simon G" first="Gaëlle" last="Simon">Gaëlle Simon</name><affiliation><nlm:affiliation>ANSES, Ploufragan-Plouzané Laboratory, Swine Virology Immunology Unit, Ploufragan, France.</nlm:affiliation></affiliation></author><author><name sortKey="Saito, Takehiko" sort="Saito, Takehiko" uniqKey="Saito T" first="Takehiko" last="Saito">Takehiko Saito</name><affiliation><nlm:affiliation>Division of Transboundary Animal Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Berhane, Yohannes" sort="Berhane, Yohannes" uniqKey="Berhane Y" first="Yohannes" last="Berhane">Yohannes Berhane</name><affiliation><nlm:affiliation>Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, Manitoba, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Ciacci Zanella, Janice" sort="Ciacci Zanella, Janice" uniqKey="Ciacci Zanella J" first="Janice" last="Ciacci-Zanella">Janice Ciacci-Zanella</name><affiliation><nlm:affiliation>Embrapa Swine and Poultry, Animal Health and Genetic Laboratory, Concórdia, SC, Brazil.</nlm:affiliation></affiliation></author><author><name sortKey="Pereda, Ariel" sort="Pereda, Ariel" uniqKey="Pereda A" first="Ariel" last="Pereda">Ariel Pereda</name><affiliation><nlm:affiliation>Instituto de Patobiología, CICVyA INTA, Hurlingham, Buenos Aires, Argentina.</nlm:affiliation></affiliation></author><author><name sortKey="Davis, C Todd" sort="Davis, C Todd" uniqKey="Davis C" first="C Todd" last="Davis">C Todd Davis</name><affiliation><nlm:affiliation>Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Donis, Ruben O" sort="Donis, Ruben O" uniqKey="Donis R" first="Ruben O" last="Donis">Ruben O. Donis</name><affiliation><nlm:affiliation>Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Webby, Richard J" sort="Webby, Richard J" uniqKey="Webby R" first="Richard J" last="Webby">Richard J. Webby</name><affiliation><nlm:affiliation>Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Vincent, Amy L" sort="Vincent, Amy L" uniqKey="Vincent A" first="Amy L" last="Vincent">Amy L. Vincent</name><affiliation><nlm:affiliation>Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="????"><PubDate><MedlineDate>2016 Nov-Dec</MedlineDate></PubDate></date><idno type="RBID">pubmed:27981236</idno><idno type="pmid">27981236</idno><idno type="doi">10.1128/mSphere.00275-16</idno><idno type="wicri:Area/PubMed/Corpus">000465</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000465</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses.</title><author><name sortKey="Anderson, Tavis K" sort="Anderson, Tavis K" uniqKey="Anderson T" first="Tavis K" last="Anderson">Tavis K. Anderson</name><affiliation><nlm:affiliation>Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Macken, Catherine A" sort="Macken, Catherine A" uniqKey="Macken C" first="Catherine A" last="Macken">Catherine A. Macken</name><affiliation><nlm:affiliation>Bioinformatics Institute, University of Auckland, Auckland, New Zealand.</nlm:affiliation></affiliation></author><author><name sortKey="Lewis, Nicola S" sort="Lewis, Nicola S" uniqKey="Lewis N" first="Nicola S" last="Lewis">Nicola S. Lewis</name><affiliation><nlm:affiliation>Department of Zoology, University of Cambridge, Cambridge, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Scheuermann, Richard H" sort="Scheuermann, Richard H" uniqKey="Scheuermann R" first="Richard H" last="Scheuermann">Richard H. Scheuermann</name><affiliation><nlm:affiliation>J. Craig Venter Institute, La Jolla, California, USA; Department of Pathology, University of California, San Diego, California, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Van Reeth, Kristien" sort="Van Reeth, Kristien" uniqKey="Van Reeth K" first="Kristien" last="Van Reeth">Kristien Van Reeth</name><affiliation><nlm:affiliation>Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.</nlm:affiliation></affiliation></author><author><name sortKey="Brown, Ian H" sort="Brown, Ian H" uniqKey="Brown I" first="Ian H" last="Brown">Ian H. Brown</name><affiliation><nlm:affiliation>Animal and Plant Health Agency, Weybridge, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Swenson, Sabrina L" sort="Swenson, Sabrina L" uniqKey="Swenson S" first="Sabrina L" last="Swenson">Sabrina L. Swenson</name><affiliation><nlm:affiliation>National Veterinary Services Laboratories, USDA-APHIS, Ames, Iowa, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Simon, Gaelle" sort="Simon, Gaelle" uniqKey="Simon G" first="Gaëlle" last="Simon">Gaëlle Simon</name><affiliation><nlm:affiliation>ANSES, Ploufragan-Plouzané Laboratory, Swine Virology Immunology Unit, Ploufragan, France.</nlm:affiliation></affiliation></author><author><name sortKey="Saito, Takehiko" sort="Saito, Takehiko" uniqKey="Saito T" first="Takehiko" last="Saito">Takehiko Saito</name><affiliation><nlm:affiliation>Division of Transboundary Animal Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Berhane, Yohannes" sort="Berhane, Yohannes" uniqKey="Berhane Y" first="Yohannes" last="Berhane">Yohannes Berhane</name><affiliation><nlm:affiliation>Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, Manitoba, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Ciacci Zanella, Janice" sort="Ciacci Zanella, Janice" uniqKey="Ciacci Zanella J" first="Janice" last="Ciacci-Zanella">Janice Ciacci-Zanella</name><affiliation><nlm:affiliation>Embrapa Swine and Poultry, Animal Health and Genetic Laboratory, Concórdia, SC, Brazil.</nlm:affiliation></affiliation></author><author><name sortKey="Pereda, Ariel" sort="Pereda, Ariel" uniqKey="Pereda A" first="Ariel" last="Pereda">Ariel Pereda</name><affiliation><nlm:affiliation>Instituto de Patobiología, CICVyA INTA, Hurlingham, Buenos Aires, Argentina.</nlm:affiliation></affiliation></author><author><name sortKey="Davis, C Todd" sort="Davis, C Todd" uniqKey="Davis C" first="C Todd" last="Davis">C Todd Davis</name><affiliation><nlm:affiliation>Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Donis, Ruben O" sort="Donis, Ruben O" uniqKey="Donis R" first="Ruben O" last="Donis">Ruben O. Donis</name><affiliation><nlm:affiliation>Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Webby, Richard J" sort="Webby, Richard J" uniqKey="Webby R" first="Richard J" last="Webby">Richard J. Webby</name><affiliation><nlm:affiliation>Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Vincent, Amy L" sort="Vincent, Amy L" uniqKey="Vincent A" first="Amy L" last="Vincent">Amy L. Vincent</name><affiliation><nlm:affiliation>Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA.</nlm:affiliation></affiliation></author></analytic><series><title level="j">mSphere</title><idno type="ISSN">2379-5042</idno></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The H1 subtype of influenza A viruses (IAVs) has been circulating in swine since the 1918 human influenza pandemic. Over time, and aided by further introductions from nonswine hosts, swine H1 viruses have diversified into three genetic lineages. Due to limited global data, these H1 lineages were named based on colloquial context, leading to a proliferation of inconsistent regional naming conventions. In this study, we propose rigorous phylogenetic criteria to establish a globally consistent nomenclature of swine H1 virus hemagglutinin (HA) evolution. These criteria applied to a data set of 7,070 H1 HA sequences led to 28 distinct clades as the basis for the nomenclature. We developed and implemented a web-accessible annotation tool that can assign these biologically informative categories to new sequence data. The annotation tool assigned the combined data set of 7,070 H1 sequences to the correct clade more than 99% of the time. Our analyses indicated that 87% of the swine H1 viruses from 2010 to the present had HAs that belonged to 7 contemporary cocirculating clades. Our nomenclature and web-accessible classification tool provide an accurate method for researchers, diagnosticians, and health officials to assign clade designations to HA sequences. The tool can be updated readily to track evolving nomenclature as new clades emerge, ensuring continued relevance. A common global nomenclature facilitates comparisons of IAVs infecting humans and pigs, within and between regions, and can provide insight into the diversity of swine H1 influenza virus and its impact on vaccine strain selection, diagnostic reagents, and test performance, thereby simplifying communication of such data. <b>IMPORTANCE</b> A fundamental goal in the biological sciences is the definition of groups of organisms based on evolutionary history and the naming of those groups. For influenza A viruses (IAVs) in swine, understanding the hemagglutinin (HA) genetic lineage of a circulating strain aids in vaccine antigen selection and allows for inferences about vaccine efficacy. Previous reporting of H1 virus HA in swine relied on colloquial names, frequently with incriminating and stigmatizing geographic toponyms, making comparisons between studies challenging. To overcome this, we developed an adaptable nomenclature using measurable criteria for historical and contemporary evolutionary patterns of H1 global swine IAVs. We also developed a web-accessible tool that classifies viruses according to this nomenclature. This classification system will aid agricultural production and pandemic preparedness through the identification of important changes in swine IAVs and provides terminology enabling discussion of swine IAVs in a common context among animal and human health initiatives.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">27981236</PMID><DateRevised><Year>2019</Year><Month>11</Month><Day>20</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2379-5042</ISSN><JournalIssue CitedMedium="Print"><Volume>1</Volume><Issue>6</Issue><PubDate><MedlineDate>2016 Nov-Dec</MedlineDate></PubDate></JournalIssue><Title>mSphere</Title><ISOAbbreviation>mSphere</ISOAbbreviation></Journal><ArticleTitle>A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">e00275-16</ELocationID><Abstract><AbstractText>The H1 subtype of influenza A viruses (IAVs) has been circulating in swine since the 1918 human influenza pandemic. Over time, and aided by further introductions from nonswine hosts, swine H1 viruses have diversified into three genetic lineages. Due to limited global data, these H1 lineages were named based on colloquial context, leading to a proliferation of inconsistent regional naming conventions. In this study, we propose rigorous phylogenetic criteria to establish a globally consistent nomenclature of swine H1 virus hemagglutinin (HA) evolution. These criteria applied to a data set of 7,070 H1 HA sequences led to 28 distinct clades as the basis for the nomenclature. We developed and implemented a web-accessible annotation tool that can assign these biologically informative categories to new sequence data. The annotation tool assigned the combined data set of 7,070 H1 sequences to the correct clade more than 99% of the time. Our analyses indicated that 87% of the swine H1 viruses from 2010 to the present had HAs that belonged to 7 contemporary cocirculating clades. Our nomenclature and web-accessible classification tool provide an accurate method for researchers, diagnosticians, and health officials to assign clade designations to HA sequences. The tool can be updated readily to track evolving nomenclature as new clades emerge, ensuring continued relevance. A common global nomenclature facilitates comparisons of IAVs infecting humans and pigs, within and between regions, and can provide insight into the diversity of swine H1 influenza virus and its impact on vaccine strain selection, diagnostic reagents, and test performance, thereby simplifying communication of such data. <b>IMPORTANCE</b> A fundamental goal in the biological sciences is the definition of groups of organisms based on evolutionary history and the naming of those groups. For influenza A viruses (IAVs) in swine, understanding the hemagglutinin (HA) genetic lineage of a circulating strain aids in vaccine antigen selection and allows for inferences about vaccine efficacy. Previous reporting of H1 virus HA in swine relied on colloquial names, frequently with incriminating and stigmatizing geographic toponyms, making comparisons between studies challenging. To overcome this, we developed an adaptable nomenclature using measurable criteria for historical and contemporary evolutionary patterns of H1 global swine IAVs. We also developed a web-accessible tool that classifies viruses according to this nomenclature. This classification system will aid agricultural production and pandemic preparedness through the identification of important changes in swine IAVs and provides terminology enabling discussion of swine IAVs in a common context among animal and human health initiatives.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Anderson</LastName><ForeName>Tavis K</ForeName><Initials>TK</Initials><Identifier Source="ORCID">0000-0002-3138-5535</Identifier><AffiliationInfo><Affiliation>Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Macken</LastName><ForeName>Catherine A</ForeName><Initials>CA</Initials><AffiliationInfo><Affiliation>Bioinformatics Institute, University of Auckland, Auckland, New Zealand.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lewis</LastName><ForeName>Nicola S</ForeName><Initials>NS</Initials><AffiliationInfo><Affiliation>Department of Zoology, University of Cambridge, Cambridge, United Kingdom.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Scheuermann</LastName><ForeName>Richard H</ForeName><Initials>RH</Initials><Identifier Source="ORCID">0000-0003-1355-892X</Identifier><AffiliationInfo><Affiliation>J. Craig Venter Institute, La Jolla, California, USA; Department of Pathology, University of California, San Diego, California, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Van Reeth</LastName><ForeName>Kristien</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Brown</LastName><ForeName>Ian H</ForeName><Initials>IH</Initials><AffiliationInfo><Affiliation>Animal and Plant Health Agency, Weybridge, United Kingdom.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Swenson</LastName><ForeName>Sabrina L</ForeName><Initials>SL</Initials><AffiliationInfo><Affiliation>National Veterinary Services Laboratories, USDA-APHIS, Ames, Iowa, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Simon</LastName><ForeName>Gaëlle</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>ANSES, Ploufragan-Plouzané Laboratory, Swine Virology Immunology Unit, Ploufragan, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Saito</LastName><ForeName>Takehiko</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Division of Transboundary Animal Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Berhane</LastName><ForeName>Yohannes</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, Manitoba, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ciacci-Zanella</LastName><ForeName>Janice</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Embrapa Swine and Poultry, Animal Health and Genetic Laboratory, Concórdia, SC, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pereda</LastName><ForeName>Ariel</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Instituto de Patobiología, CICVyA INTA, Hurlingham, Buenos Aires, Argentina.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Davis</LastName><ForeName>C Todd</ForeName><Initials>CT</Initials><AffiliationInfo><Affiliation>Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Donis</LastName><ForeName>Ruben O</ForeName><Initials>RO</Initials><AffiliationInfo><Affiliation>Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Webby</LastName><ForeName>Richard J</ForeName><Initials>RJ</Initials><AffiliationInfo><Affiliation>Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vincent</LastName><ForeName>Amy L</ForeName><Initials>AL</Initials><AffiliationInfo><Affiliation>Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>HHSN266200700005C</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>HHSN272201400006C</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>HHSN272201400008C</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>12</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>mSphere</MedlineTA><NlmUniqueID>101674533</NlmUniqueID><ISSNLinking>2379-5042</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">H1N1</Keyword><Keyword MajorTopicYN="N">H1N2</Keyword><Keyword MajorTopicYN="N">influenza A virus</Keyword><Keyword MajorTopicYN="N">molecular epidemiology</Keyword><Keyword MajorTopicYN="N">nomenclature</Keyword><Keyword MajorTopicYN="N">swine</Keyword><Keyword MajorTopicYN="N">virus evolution</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>09</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>11</Month><Day>10</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>12</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>12</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>12</Month><Day>17</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27981236</ArticleId><ArticleId IdType="doi">10.1128/mSphere.00275-16</ArticleId><ArticleId IdType="pii">mSphere00275-16</ArticleId><ArticleId IdType="pmc">PMC5156671</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Virus Genes. 2009 Oct;39(2):176-85</Citation><ArticleIdList><ArticleId IdType="pubmed">19597980</ArticleId></ArticleIdList></Reference><Reference><Citation>Curr Top Microbiol Immunol. 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